Maria -
I would modify the hydrogen's standard parameters as the very last option
since you will disrupt the consistency of your force field. Based on your
snapshots, I still suppose that your angles (like H-O-R) are not healthy. I
would check the particular values of these angles after your minimization
and double-check what is written in the topology file.
The atom types, theoretically, can be assigned incorrectly even it is
done automatically. As for the Mulliken charges, I do not believe them
anyway... :-)
Cordially,
Vitaly Chaban
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
On Thu, Jul 12, 2012 at 7:23 PM, Maria Minakova
<mariabiophysics.gmail.com>wrote:
> thank you for responding quickly!
> I have no other choice, than using mulliken. resp produced very
> unrealistic partial charges for buried transition metal atoms, according to
> synthetic chemists I consulted with.
> Mulliken on the other hand looked more plausible. I compared the atoms on
> the compound periphery and they fit well with the resp ones, which gave me
> hope that they should not be that bad after all.
> Angles were not modified for any standard atoms, so they are given by
> gaff.
> As I mentioned before the atom types were also asigned automatically using
> gaff.
> Snapshots are attached.
> I would appreciate any feedback or suggestions. Maybe i should run
> minimization in some special way?
>
>
>
> On Jul 12, 2012, at 7:05 PM, Dr. Vitaly V. G. Chaban wrote:
>
> I think everyone will tell you that using the Mulliken charges is not
> an appropriate practice in classical MD, since your electrostatics
> will be totally unrealistic.
>
> It is difficult to judge why hydrogens collapse onto oxygens without
> the particular snapshots. Perhaps, there is some erratum in angles or
> dihedrals for these atoms?
>
>
> Dr. Vitaly V. Chaban, 430 Hutchison Hall
> Dept. Chemistry, University of Rochester
> 120 Trustee Road, Rochester, NY 14627-0216
> THE UNITED STATES OF AMERICA
>
>
>
> On Thu, Jul 12, 2012 at 6:23 PM, Maria Minakova
> <mariabiophysics.gmail.com> wrote:
>
> Hello,
>
>
> I am minimizing a complex synthetic compound, which also has phosphonic
> acid groups attached to it:
>
> OH
>
> |
>
> R - P = O
>
> |
>
> OH
>
> The automatic atom type assignment (gaff) put (py) atom type for central
> P, (o) for double bond O, (oh) for O in OH fragment, and (ho) for H in OH
> fragment.
>
> I did not put any restrictions for minimization, and within fist 1000
> steps hydrogens collapsed onto neighboring oxygens, which is not supposed
> to happen.
>
> I wonder if there is something wrong with my parametrization or
> minimization script.
>
> Any ideas or suggestions?..
>
>
> additional info:
>
> Partial charges were assigned by mulliken method (resp didn't work well
> with the rest of this compound).
>
>
>
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Received on Thu Jul 12 2012 - 17:30:03 PDT
